Medullary thyroid carcinoma (MTC) is a rare tumor arising from parafollicular C-cells. The oncocytic variant of MTC is an extremely rare diagnosis, with less than 20 cases reported. Here we present the case of a 36-year-old male patient with complaints of neck swelling and dysphagia. On fine needle aspiration cytology (FNAC), a Hürthle cell neoplasm was suggested. Finally with histopathology and immunohistochemistry (IHC), a diagnosis of MTC oncocytic variant was established. This tumor can be easily misdiagnosed for any thyroid Hürthle cell lesions. An accurate diagnosis is important because MTC has different treatment protocols, and its oncocytic variant is expected to be associated with poorer patient survival. Thus, the oncocytic variant of MTC is a difficult diagnosis on FNAC. Histopathology and relevant IHC markers are necessary for a correct diagnosis.